VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 14 2005 - 10:11:34 CST

Hi,
  There's no built-in script for this, but you might find this
article (quick google result) helpful in writing a script for this:
  http://oemagazine.com/fromthemagazine/nov05/tutorial.html

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 13, 2005 at 04:43:03PM -0500, Samuel Flores wrote:
> Hi Guys,
>
> Is there a tcl function to extract the equivalent x,y,z euler angles from a
> transformation matrix?
>
> Thanks
>
> Sam
>
> Samuel Flores
> Graduate Student
> Gerstein Lab
>
> Office:
> Bass 437
> 266 Whitney Avenue
> New Haven, CT 06520
> 203.432.5405
>
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>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> John Stone
> Sent: Wednesday, October 12, 2005 6:04 PM
> To: mashaojie163
> Cc: vmd
> Subject: Re: vmd-l: Can vmd do symmetry operation?
>
>
> Hi,
> VMD doesn't have any built-in symmetry handling code. It only includes
> the ability to perform matrix transformations on the atom coordinates.
> While this is general enough to do what you are probably wanting to do,
> it doesn't provide a usable way to operate using symmetry records in the
> PDB for example. If someone knows of scripts or libraries that can
> emit the appropriate transformation matrices for a given set of symmetry
> operators, that'd be very useful in adding such a feature or a plugin
> for this specific purpose.
>
> John
>
> On Wed, Oct 12, 2005 at 10:49:00AM +0800, mashaojie163 wrote:
> > Hi:
> > I want to do symmetry operation by use of vmd. What should I do? I know
> I can use command "$sel move [transabout vec amount]" to accomplish rotation
> amount by vec . But How can I do reflecting operation by a plane or a
> point.
> > Can vmd do symmetry operation by use of GRoup Theory?
> >
> Ma shaojie
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078